Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription.

Abstract

In leiomyosarcoma class IIa HDACs (histone deacetylases) bind MEF2 and convert these transcription factors into repressors to sustain proliferation. Disruption of this complex with small molecules should antagonize cancer growth. NKL54, a PAOA (pimeloylanilide o-aminoanilide) derivative, binds a hydrophobic groove of MEF2, which is used as a docking site by class IIa HDACs. However, NKL54 could also act as HDAC inhibitor (HDACI). Therefore, it is unclear which activity is predominant. Here, we show that NKL54 and similar derivatives are unable to release MEF2 from binding to class IIa HDACs. Comparative transcriptomic analysis classifies these molecules as HDACIs strongly related to SAHA/vorinostat. Low expressed genes are upregulated by HDACIs, while abundant genes are repressed. This transcriptional resetting correlates with a reorganization of H3K27 acetylation around the transcription start site (TSS). Among the upregulated genes there are several BH3-only family members, thus explaining the induction of apoptosis. Moreover, NKL54 triggers the upregulation of MEF2 and the downregulation of class IIa HDACs. NKL54 also increases the binding of MEF2D to promoters of genes that are upregulated after treatment. In summary, although NKL54 cannot outcompete MEF2 from binding to class IIa HDACs, it supports MEF2-dependent transcription through several actions, including potentiation of chromatin binding.

• Authors: Martina Minisini, Eros Di Giorgio, Emanuela Kerschbamer, Emiliano Dalla, Massimo Faggiani, Elisa Franforte, Franz-Josef Meyer-Almes, Rino Ragno, Lorenzo Antonini, Antonello Mai, Francesco Fiorentino, Dante Rotili, Monica Chinellato, Stefano Perin, Laura Cendron, Christian X Weichenberger, Alessandro Angelini, Claudio Brancolini
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 50 Issue 5 Pg. 2566-2586 (03 21 2022) ISSN: 1362-4962 [Electronic] England
• PMID: 35150567 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• Histone Deacetylase Inhibitors
• MEF2 Transcription Factors
• Vorinostat
• Histone Deacetylases

Topics

• Acetylation
• Histone Deacetylase Inhibitors (chemistry, pharmacology)
• Histone Deacetylases (metabolism)
• MEF2 Transcription Factors (genetics)
• Transcriptome
• Vorinostat (pharmacology)